Browsing by Author "Sener, Duygu Dede"

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A Content-Based Retrieval Framework for Whole Metagenome Sequencing Samples
(2018) Sener, Duygu Dede; Santoni, Daniele; Felici, Giovanni; Ogul, Hasan; 30367805
Finding similarities and differences between metagenomic samples within large repositories has been rather a significant issue for researchers. Over the recent years, content-based retrieval has been suggested by various studies from different perspectives. In this study, a content-based retrieval framework for identifying relevant metagenomic samples is developed. The framework consists of feature extraction, selection methods and similarity measures for whole metagenome sequencing samples. Performance of the developed framework was evaluated on given samples. A ground truth was used to evaluate the system performance such that if the system retrieves patients with the same disease, -called positive samples-, they are labeled as relevant samples otherwise irrelevant. The experimental results show that relevant experiments can be detected by using different fingerprinting approaches. We observed that Latent Semantic Analysis (LSA) Method is a promising fingerprinting approach for representing metagenomic samples and finding relevance among them. Source codes and executable files are available at www.baskent.edu.tr/similar to hogul/WMS_retrieval.rar
Inferring Similarity between Time-Series Microarrays: A Content-based Approach
(2015) Sener, Duygu Dede; Ogul, Hasan; 0000-0001-6766-4977
Public repositories for gene expression studies have been growing rapidly in the last decade. Retrieval of gene expression experiments based on textual descriptions does not provide sufficient data for biologists and clinicians. Content-based search has recently become more desirable in retrieving similar experiments. Current methods for content-based retrieval cannot address the problem of profiling the gene behaviors in multiple measurement points, i.e. in time course. This study, to the best of our knowledge, is the first attempt to build a fingerprint for each gene by considering all time points to infer its time-course profile to represent the experiment content in an information retrieval framework. An empirical study is performed on a large dataset of Arabidopsis microarrays from Gene Expression Omnibus (GEO). Experimental results show that relevant experiments are retrieved based on content similarity.
Multiclass Classification of Brain Cancer with Machine Learning Algorithms
(2020) Erkal, Begum; Basak, Selen; Ciloglu, Alper; Sener, Duygu Dede
Brain cancer is one the most important disease to be treated all around the world. Classification of brain cancer using machine learning techniques has been widely studied by researchers. Microarray gene expression data are commonly used medical data to get observable results in this manner. In this study, multiclass classification of brain cancer is aimed by using different machine learning approaches. Some preprocessing methods were applied to get improved results. According to the result, feature selection has greatly affected the overall performance of each method in terms of overall accuracy and per class accuracy. Experimental results show that Multilayer Perceptron (MP) method has higher accuracy rate compared with other machine learning methods.
Text-based Experiment Retrieval in Genomic Databases
(2022) Sener, Duygu Dede; Ogul, Hasan; Basak, Selen; https://orcid.org/0000-0001-6766-4977
With the growing number of genomic data in public repositories, efficient search methodologies have become a basic need to reach the relevant genomic data. However, this need cannot be fulfilled with the current repositories because they offer a limited search option which is a lexical matching of textual descriptions or metadata of the experiments. This technique is insufficient to get the required information needed to detect similarities between experiments within a large data collection. Due to the limitation of the existing repositories, in this study, we develop a text-based experiment retrieval framework by using both lexical and semantic similarity approaches to find similarities between experiments, and their retrieval performance was compared. This study is the first attempt to use text-driven semantic analysis approaches for developing a retrieval framework for experiments. An empirical study was conducted on a large textual description of Arabidopsis microarray experiments from the Gene Expression Omnibus database. In the proposed model, Jaccard similarity was used as a lexical similarity approach; Latent Semantic Analysis, Probabilistic Latent Semantic Analysis and Latent Dirichlet allocation were used as semantic similarity approaches to detect similarities between the textual descriptions of the experiments. According to the experimental results, relevant experiments can be retrieved successfully by text-driven semantic similarity approaches compared with the lexical similarity approach.